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    SEC Form SC 13D/A filed by Omega Therapeutics Inc. (Amendment)

    2/27/23 5:02:08 PM ET
    $OMGA
    Biotechnology: Biological Products (No Diagnostic Substances)
    Health Care
    Get the next $OMGA alert in real time by email
    SC 13D/A 1 d459978dsc13da.htm SC 13D/A SC 13D/A

     

     

    SECURITIES AND EXCHANGE COMMISSION

    WASHINGTON, D.C. 20549

     

     

    SCHEDULE 13D

    UNDER THE SECURITIES EXCHANGE ACT OF 1934

    (Amendment No. 1)*

     

     

    OMEGA THERAPEUTICS, INC.

    (Name of Issuer)

    Common Stock, $0.001 par value per share

    (Title of Class of Securities)

    68217N 105

    (CUSIP Number)

    Noubar B. Afeyan, Ph.D.

    Flagship Pioneering

    55 Cambridge Parkway, Suite 800E

    Cambridge, MA 02142

    (617) 868-1888

    (Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

    February 22, 2023

    (Date of Event Which Requires Filing of Statement on Schedule 13D)

     

     

    If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), checking the following box.  ☐

     

    *

    The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

    The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

     

     

     


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship V VentureLabs Rx Fund, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      1,088,470

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      1,088,470

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      1,088,470

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      2.0%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Ventures Fund V, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      5,896,386

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      5,896,386

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      5,896,386

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      10.7%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Ventures Fund V General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      6,984,856

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      6,984,856

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      6,984,856

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      12.7%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Fund VI, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      8,617,413

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      8,617,413

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      8,617,413

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      15.7%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Fund VI General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      8,617,413

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      8,617,413

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      8,617,413

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      15.7%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Nutritional Health LTP Fund, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      970,588

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      970,588

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      970,588

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      1.8%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Nutritional Health LTP Fund General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      970,588

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      970,588

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      970,588

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      1.8%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Special Opportunities Fund II, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      7,508,693

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      7,508,693

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      7,508,693

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      13.6%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Special Opportunities Fund II General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      7,508,693

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      7,508,693

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      7,508,693

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

      13.6%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      FPN, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Ontario, Canada

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      1,617,646

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      1,617,646

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      1,617,646

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    2.9%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      FPN General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      1,617,646

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      1,617,646

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      1,617,646

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    2.9%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship VentureLabs V, LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      2,197,059

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      2,197,059

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      2,197,059

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    4.0%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      VentureLabs V Manager LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      2,197,059

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      2,197,059

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      2,197,059

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    4.0%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Fund VII, L.P.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      WC

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      1,329,324

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      1,329,324

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      1,329,324

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    2.4%

    (14)  

      Type of Reporting Person (See Instructions):

     

      PN


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering Fund VII General Partner LLC

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      1,329,324

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      1,329,324

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      1,329,324

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    2.4%

    (14)  

      Type of Reporting Person (See Instructions):

     

      OO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Flagship Pioneering, Inc.

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      Delaware

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      0

         (8)   

      Shared Voting Power

     

      22,240,723

         (9)   

      Sole Dispositive Power

     

      0

       (10)   

      Shared Dispositive Power

     

      22,240,723

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      22,240,723

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    40.4%

    (14)  

      Type of Reporting Person (See Instructions):

     

      CO


    CUSIP No. 68217N 105

     

      (1)    

      Name of Reporting Persons:

     

      Noubar Afeyan

      (2)  

      Check the Appropriate Box if a Member of a Group (See Instructions):

      (a)  ☐        (b)  ☒

     

      (3)  

      SEC Use Only:

     

      (4)  

      Source of Funds (See Instructions):

     

      AF

      (5)  

      Check Box if Disclosure of Legal Proceedings is Required Pursuant to Items 2(d) or 2(e):

     

      ☐

      (6)  

      Citizenship or Place of Organization:

     

      United States of America

    NUMBER OF

    SHARES

     BENEFICIALLY 

    OWNED BY

    EACH

    REPORTING

    PERSON

    WITH:

     

         (7)     

      Sole Voting Power

     

      19,852*

         (8)   

      Shared Voting Power

     

      29,225,579

         (9)   

      Sole Dispositive Power

     

      19,852*

       (10)   

      Shared Dispositive Power

     

      29,225,579

    (11)    

      Aggregate Amount Beneficially Owned by Each Reporting Person:

     

      29,245,431*

    (12)  

      Check Box if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

     

      ☐

    (13)  

      Percent of Class Represented by Amount in Row (11):

     

    53.2%

    (14)  

      Type of Reporting Person (See Instructions):

     

    IN

     

    *

    Includes 19,852 shares of Common Stock underlying stock options exercisable within 60 days of this Statement, which are deemed outstanding pursuant to SEC Rule 13-3(d)(1)(i).


    CUSIP No. 68217N 105

     

    EXPLANATORY NOTE

    This Amendment No. 1 (this “Amendment”) amends and supplements the Schedule 13D (the “Schedule 13D”) originally filed by the Reporting Persons (as defined below) on August 5, 2021 relating to the shares of common stock, $0.001 par value per share (“Common Stock”), of Omega Therapeutics Inc. (the “Issuer” or the “Company”). The address of the principal executive offices of the Issuer is 20 Acorn Park Drive, Cambridge, MA 02140.

     

    ITEM 2.

    IDENTITY AND BACKGROUND

    Item 2 of the Schedule 13D is hereby amended and restated as follows:

    This Schedule 13D is being filed by the following persons (each a “Reporting Person”):

     

      i.

    Flagship V VentureLabs Rx Fund, L.P., a Delaware limited partnership (“Flagship Fund V Rx”). The general partner of Flagship Fund V Rx is Flagship Ventures Fund V General Partner LLC, a Delaware limited liability company (“Flagship Fund V GP”).

     

      ii.

    Flagship Ventures Fund V, L.P., a Delaware limited partnership (“Flagship Fund V”). The general partner of Flagship Fund V is Flagship Fund V GP.

     

      iii.

    Flagship Fund V GP. Noubar B. Afeyan, Ph.D. (“Dr. Afeyan”) is the sole manager of Flagship Fund V GP.

     

      iv.

    Flagship Pioneering Fund VI, L.P., a Delaware limited partnership (“Flagship Fund VI”). The general partner of Flagship Fund VI is Flagship Pioneering Fund VI General Partner LLC, a Delaware limited liability company (“Flagship Fund VI GP”).

     

      v.

    Flagship Fund VI GP. The manager of Flagship Fund VI GP is Flagship Pioneering, Inc., a Delaware corporation (“Flagship Pioneering”).

     

      vi.

    Nutritional Health LTP Fund, L.P., a Delaware limited partnership (“Nutritional LTP”). The general partner of Nutritional LTP is Nutritional Health LTP Fund General Partner LLC, a Delaware limited liability company (“Nutritional LTP GP”).

     

      vii.

    Nutritional LTP GP. Flagship Pioneering is the sole manager of Nutritional LTP GP.

     

      viii.

    Flagship Pioneering Special Opportunities Fund II, L.P., a Delaware limited partnership (“Flagship Opportunities Fund II”). The general partner of Flagship Opportunities Fund II is Flagship Pioneering Special Opportunities Fund II General Partner LLC, a Delaware limited liability company (“Flagship Opportunities Fund II GP”).

     

      ix.

    Flagship Opportunities Fund II GP. The manager of Flagship Opportunities Fund II GP is Flagship Pioneering.

     

      x.

    FPN, L.P., a limited partnership organized under the laws of Ontario (“FPN Fund”). The general partner of FPN Fund is FPN General Partner LLC, a Delaware limited liability company (“FPN GP”).

     

      xi.

    FPN GP. The manager of FPN GP is Flagship Pioneering.

     

      xii.

    Flagship VentureLabs V, LLC, a Delaware limited liability company (“VentureLabs V”). The manager of VentureLabs V is VentureLabs V Manager LLC, a Delaware limited liability company (“VentureLabs V Manager”).

     

      xiii.

    VentureLabs V Manager. The manager of VentureLabs V Manager is Flagship Pioneering.

     

      xiv.

    Flagship Pioneering Fund VII, L.P., a Delaware limited partnership (“Flagship Fund VII” and together with Flagship Fund V Rx, Flagship Fund V, Flagship Fund VI, Nutritional LTP, Flagship Opportunities Fund II, FPN Fund and VentureLabs V, the “Flagship Funds”). The general partner of Flagship Fund VII is Flagship Pioneering Fund VII General Partner LLC, a Delaware limited liability company (“Flagship Fund VII GP”).


    CUSIP No. 68217N 105

     

      xv.

    Flagship Fund VII GP. The manager of Flagship Fund VII GP is Flagship Pioneering.

     

      xvi.

    Flagship Pioneering. Dr. Afeyan is the CEO, sole shareholder and director of Flagship Pioneering.

     

      xvii.

    Dr. Afeyan, a citizen of the United States of America.

    The principal business of each Reporting Person is the venture capital investment business. The principal business address of each Reporting Person is 55 Cambridge Parkway, Suite 800E, Cambridge, Massachusetts 02142.

    During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors).

    During the last five years, none of the Reporting Persons has been party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding were or are subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

     

    ITEM 4.

    PURPOSE OF TRANSACTION

    Item 4 of the Schedule 13D is hereby amended to include the following:

    Securities Purchase Agreement

    On February 22, 2023, the Company entered into a Securities Purchase Agreement (the “Purchase Agreement”) with certain purchasers named therein (collectively, the “Purchasers”), including Flagship Opportunities Fund II and Flagship Fund VII. Pursuant to the Purchase Agreement, the Company agreed to issue and sell in a registered direct offering (the “Offering”) an aggregate of 6,920,415 shares of the Common Stock at a purchase price of $5.78 per share to the Purchasers, pursuant to an effective shelf registration statement on Form S-3 (File No. 333-268254) and a related prospectus supplement filed with the Securities and Exchange Commission. The closing of the Offering was subject to the satisfaction of customary closing conditions and occurred on February 27, 2023. In connection with the Offering, Flagship Opportunities Fund II and Flagship Fund VII purchased 1,993,986 shares and 1,329,324 shares of Common Stock, respectively.

    The Purchase Agreement contains customary representations, warranties and agreements by the Company, customary conditions to closing, indemnification obligations of the Company and the Purchasers, including for liabilities under the Securities Act of 1933, as amended, other obligations of the parties and termination provisions.

    The foregoing description of the Purchase Agreement is not complete and is qualified in its entirety by reference to the full text of the Purchase Agreement, a form of which is filed as Exhibit 2 hereto and is incorporated by reference herein.

     

    ITEM 5.

    INTEREST IN SECURITIES OF THE ISSUER

    Item 5(a)-(c) of the Schedule 13D is hereby amended and restated as follows:

    (a)-(b) The information set forth in rows 7 through 13 of the cover pages to this Schedule 13D is incorporated by reference. The percentage set forth in row 13 is based on 55,012,649 shares of Common Stock outstanding, as reported in the Issuer’s Form 424(b)(5) prospectus supplement filed with the Securities and Exchange Commission on February 23, 2023.

    Flagship Fund V Rx directly holds 1,088,470 shares of Common Stock. Flagship Fund V directly holds 5,896,386 shares of Common Stock. Flagship Fund V GP, as the general partner of each of Flagship Fund V Rx and Flagship Fund V, may be deemed to beneficially own the shares directly held by Flagship Fund V Rx and Flagship Fund V.

    Flagship Fund VI directly holds 8,617,413 shares of Common Stock. Flagship Fund VI GP, as general partner of Flagship Fund VI, may be deemed to beneficially own the shares directly held by Flagship Fund VI.

    Nutritional LTP directly holds 970,588 shares of Common Stock. Nutritional LTP GP, as general partner of Nutritional LTP, may be deemed to beneficially own the shares directly held by Nutritional LTP.


    CUSIP No. 68217N 105

     

    Flagship Opportunities Fund II directly holds 7,508,693 shares of Common Stock. Flagship Opportunities Fund II GP, as general partner of Flagship Opportunities Fund II, may be deemed to beneficially own the shares directly held by Flagship Opportunities Fund II.

    FPN Fund directly holds 1,617,646 shares of Common Stock. FPN GP, as general partner of FPN Fund, may be deemed to beneficially own the shares directly held by FPN Fund.

    VentureLabs V directly holds 2,197,059 shares of Common Stock. VentureLabs V Manager, as manager of VentureLabs V, may be deemed to beneficially own the shares directly held by VentureLabs V.

    Flagship Fund VII directly holds 1,329,324 shares of Common Stock. Flagship Fund VII GP, as general partner of Flagship Fund VII, may be deemed to beneficially own the shares directly held by Flagship Fund VII.

    Flagship Pioneering, as the manager of each of Flagship Fund VI GP, Nutritional LTP GP, Flagship Opportunities II GP, FPN GP, VentureLabs V Manager and Flagship Fund VII GP, may be deemed to beneficially own the shares held directly by Flagship Fund VI, Nutritional LTP, Flagship Opportunities Fund II, FPN Fund, VentureLabs V and Flagship Fund VII.

    Dr. Afeyan may be deemed to beneficially own 19,852 shares of Common Stock underlying stock options exercisable within 60 days of this Statement, and as the sole manager of Flagship Fund V GP and as CEO, sole shareholder and director of Flagship Pioneering, may be deemed to beneficially own the shares directly held by the Flagship Funds.

    (c) Except as reported in Item 4 of this Statement, none of the Reporting Persons have effected transactions in the Common Stock of the Issuer during the past 60 days.

     

    ITEM 6.

    CONTRACTS, ARRANGEMENTS, UNDERSTANDINGS OR RELATIONSHIPS WITH RESPECT TO SECURITIES OF THE ISSUER

    Item 6 of the Schedule 13D is hereby amended to include the following:

    The information set forth in Item 4 above is incorporated by reference into this Item 6.

     

    ITEM 7.

    MATERIAL TO BE FILED AS EXHIBITS

     

    Exhibit 1    Joint Filing Agreement (filed herewith).
    Exhibit 2    Form of Securities Purchase Agreement (incorporated by reference to Exhibit 10.1 to the Issuer’s Current Report on Form 8-K, as filed with the Securities and Exchange Commission on February 23, 2023).


    SIGNATURE

    After reasonable inquiry and to the best of its knowledge and belief, the undersigned certifies that the information set forth in this Statement is true, complete and correct.

    Dated: February 27, 2023

     

    FLAGSHIP V VENTURELABS RX FUND, L.P.
    By:   Flagship Ventures Fund V General Partner LLC
    Its:   General Partner
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Manager
    FLAGSHIP VENTURES FUND V, L.P.
    By:   Flagship Ventures Fund V General Partner LLC
    Its:   General Partner
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Manager
    FLAGSHIP PIONEERING FUND VI, L.P.
    By:   Flagship Pioneering Fund VI General Partner LLC
    Its:   General Partner
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    NUTRITIONAL HEALTH LTP FUND, L.P.
    By:   Nutritional Health LTP Fund General Partner LLC
    Its:   General Partner
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer


    FLAGSHIP PIONEERING SPECIAL OPPORTUNITIES FUND II, L.P.
    By:   Flagship Pioneering Special Opportunities Fund II General Partner LLC
    Its:   General Partner
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FPN, L.P.
    By:   FPN General Partner LLC
    Its:   General Partner
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FLAGSHIP VENTURELABS V, LLC
    By:   VentureLabs V Manager LLC
    Its:   Manager
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FLAGSHIP PIONEERING FUND VII, L.P.
    By:   Flagship Pioneering Fund VII General Partner LLC
    Its:   General Partner
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FLAGSHIP VENTURES FUND V GENERAL PARTNER LLC
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Manager
    FLAGSHIP PIONEERING FUND VI GENERAL PARTNER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer


    NUTRITIONAL HEALTH LTP FUND GENERAL PARTNER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Manager
    FLAGSHIP PIONEERING SPECIAL OPPORTUNITIES FUND II GENERAL PARTNER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FPN GENERAL PARTNER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    VENTURELABS V MANAGER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer
    FLAGSHIP PIONEERING FUND VII GENERAL PARTNER LLC
    By:   Flagship Pioneering, Inc.
    Its:   Manager
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer


    FLAGSHIP PIONEERING, INC.
    By:  

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.
    Title:   Chief Executive Officer

    /s/ Noubar B. Afeyan, Ph.D.

    Name:   Noubar B. Afeyan, Ph.D.

     

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      Ampersand's AND™ Platform will be used to identify programmed biologics for the treatment of obesity-related targets Montai's CONECTA™ AI platform will be used to identify small molecules directed to a potential Non-Small Cell Lung Cancer-related target   Collaborations will leverage Pfizer's deep expertise in early discovery and development for cardiometabolic and cancer treatments, two priority therapeutic areas for the company CAMBRIDGE, Mass., Nov. 20, 2024 /PRNewswire/ -- Flagship Pioneering, the bioplatform innovation company, today announced  Ampersand Biomedicines and Montai Therapeutics have entered into agreements to identify targeted molecules that could potentially be further dev

      11/20/24 6:30:00 AM ET
      $FHTX
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      Biotechnology: Pharmaceutical Preparations
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      Biotechnology: Biological Products (No Diagnostic Substances)

    $OMGA
    Analyst Ratings

    Analyst ratings in real time. Analyst ratings have a very high impact on the underlying stock. See them live in this feed.

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    • Omega Therapeutics downgraded by Raymond James

      Raymond James downgraded Omega Therapeutics from Outperform to Mkt Perform

      11/15/24 9:11:43 AM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • Raymond James initiated coverage on Omega Therapeutics with a new price target

      Raymond James initiated coverage of Omega Therapeutics with a rating of Outperform and set a new price target of $12.00

      6/18/24 7:37:53 AM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • Jefferies resumed coverage on Omega Therapeutics with a new price target

      Jefferies resumed coverage of Omega Therapeutics with a rating of Buy and set a new price target of $15.00 from $18.00 previously

      5/25/23 7:51:53 AM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    SEC Filings

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    • SEC Form EFFECT filed by Omega Therapeutics Inc.

      EFFECT - Omega Therapeutics, Inc. (0001850838) (Filer)

      3/26/25 12:15:12 AM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • SEC Form POS AM filed by Omega Therapeutics Inc.

      POS AM - Omega Therapeutics, Inc. (0001850838) (Filer)

      3/21/25 4:04:35 PM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • SEC Form S-8 POS filed by Omega Therapeutics Inc.

      S-8 POS - Omega Therapeutics, Inc. (0001850838) (Filer)

      3/21/25 4:03:00 PM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    Large Ownership Changes

    This live feed shows all institutional transactions in real time.

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    • SEC Form SC 13G/A filed by Omega Therapeutics Inc. (Amendment)

      SC 13G/A - Omega Therapeutics, Inc. (0001850838) (Subject)

      2/12/24 12:03:27 PM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • SEC Form SC 13G/A filed by Omega Therapeutics Inc. (Amendment)

      SC 13G/A - Omega Therapeutics, Inc. (0001850838) (Subject)

      2/9/24 4:17:05 PM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    • SEC Form SC 13G/A filed by Omega Therapeutics Inc. (Amendment)

      SC 13G/A - Omega Therapeutics, Inc. (0001850838) (Subject)

      2/9/24 9:28:31 AM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
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    Leadership Updates

    Live Leadership Updates

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    • Flagship Pioneering Appoints Angela Hwang as CEO-Partner and Chief Executive Officer of Metaphore Biotechnologies

      CAMBRIDGE, Mass., Nov. 20, 2024 /PRNewswire/ -- Flagship Pioneering, the bioplatform innovation company, and Metaphore Biotechnologies, a Flagship-founded biotechnology company designing novel therapeutics by combining machine learning and molecular mimicry, today announced that Angela Hwang, MBA, will join Flagship Pioneering as CEO-Partner, and Metaphore as Chief Executive Officer, effective January 1, 2025. Most recently, Hwang served as Chief Commercial Officer and President of the Global Biopharmaceuticals Business at Pfizer. During her tenure at Pfizer, Hwang helped brin

      11/20/24 8:00:00 AM ET
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      Biotechnology: Pharmaceutical Preparations
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      Biotechnology: Biological Products (No Diagnostic Substances)
    • Omega Therapeutics Announces Successful Completion of Phase 1 Trial for Novel Epigenomic Controller, Prioritized Pipeline, Leadership Changes, and Third Quarter 2024 Financial Results

      Established clinical proof-of-mechanism and validation of epigenomic controllers as potential new class of medicines from completed Phase 1 MYCHELANGELO™ I trial for c-MYC in HCC; Company exploring strategic partnership opportunities for Phase 2 development of OTX-2002Company is focusing capital resources on three prioritized programs that reflect Omega's unique value proposition to enable precision epigenomic control for potential therapeutic advantages versus existing modalitiesBoard has appointed Kaan Certel, Ph.D., as Omega's President and Chief Executive Officer, and Jennifer Nelson, Ph.D., as Chief Scientific OfficerCompany is pursuing strategic partnership opportunities to support dev

      11/14/24 4:05:00 PM ET
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      Biotechnology: Biological Products (No Diagnostic Substances)
      Health Care
    • Flagship Pioneering Appoints Craig Williams as CEO-Partner and Chief Executive Officer of Apriori Bio

      Williams was promoted from Operating Partner at Flagship Pioneering and President at Apriori Bio Apriori Bio has made significant progress in 2024, including securing a collaboration with CEPI, assembling a world class board of directors and building out an early pipeline of prospective vaccines CAMBRIDGE, Mass., Nov. 13, 2024 /PRNewswire/ -- Flagship Pioneering, the bioplatform innovation company, and Apriori Bio, a biotechnology company aimed at providing humanity with variant-resilient protection against rapidly-evolving viruses, today announced that Craig Williams, MBA, has been promoted to CEO-Partner at Flagship Pioneering and Chief Executive Officer of Apriori.

      11/13/24 8:00:00 AM ET
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      Biotechnology: Pharmaceutical Preparations
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      Biotechnology: Biological Products (No Diagnostic Substances)